Corpus overview


MeSH Disease

COVID-19 (1)

HGNC Genes

There are no HGNC terms in the subcorpus

SARS-CoV-2 proteins

ORF9c (2)

ORF3a (1)

ORF3b (1)

ORF9b (1)


SARS-CoV-2 Proteins
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    Conflicting and Ambiguous Names of Overlapping ORFs in SARS-CoV- 2: A Homology-Based Resolution

    Authors: Irwin Jungreis; Chase W. Nelson; Zachary Ardern; Yaara Finkel; Nevan J. Krogan; Kei Sato; John Ziebuhr; Noam Stern-Ginossar; Angelo Pavesi; Andrew E. Firth; Alexander E. Gorbalenya; Manolis Kellis

    id:10.20944/preprints202012.0048.v1 Date: 2020-12-02 Source:

    At least six small alternate-frame open reading frames (ORFs) overlapping well-characterized SARS-CoV-2 genes have been hypothesized to encode accessory proteins. Researchers have used different names for the same ORF or the same name for different ORFs, resulting in erroneous homological and functional inferences. We propose standard names for these ORFs and their shorter isoforms, developed in consultation with the Coronaviridae Study Group of the ICTV. We recommend calling the 39 codon Spike-overlapping ORF ORF2b; the 41, 57, and 22 codon ORF3a PROTEIN-overlapping ORFs ORF3c, ORF3d, and ORF3b PROTEIN; the 33 codon ORF3d isoform ORF3d-2; and the 97 and 73 codon Nucleocapsid-overlapping ORFs ORF9b PROTEIN and ORF9c PROTEIN. Finally, we document conflicting usage of the name ORF3b PROTEIN in 32 studies, and consequent erroneous inferences, stressing the importance of reserving identical names for homologs. We recommend that authors referring to these ORFs provide lengths and coordinates to minimize ambiguity due to prior usage of alternative names.

    SARS-CoV-2 ORF9c PROTEIN Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells

    Authors: Ana Dominguez Andres; Yongmei Feng; Alexandre Rosa Campos; Jun Yin; Chih-Cheng Yang; Brian James; Rabi Murad; Hyungsoo Kim; Aniruddha J Deshpande; David E Gordon; Nevan J Krogan; Raffaella Pippa; Denise Doolan; Joseph Torresi; Weisan Chen; Linda Wakim; Allen Cheng; Jan Petersen; Jamie Rossjohn; Adam K Wheatley; Stephen Kent; Louise Rowntree; Katherine Kedzierska; Mengge Lyu; Guixiang Xiao; Xia Xu; Weigang Ge; Jiale He; Jun Fan; Junhua Wu; Meng Luo; Xiaona Chang; Huaxiong Pan; Xue Cai; Junjie Zhou; Jing Yu; Huanhuan Gao; Mingxing Xie; Sihua Wang; Guan Ruan; Hao Chen; Hua Su; Heng Mei; Danju Luo; Dashi Zhao; Fei Xu; Yan Li; Yi Zhu; Jiahong Xia; Yu Hu; Tiannan Guo

    doi:10.1101/2020.08.18.256776 Date: 2020-08-19 Source: bioRxiv

    Disrupted antiviral immune responses are associated with severe COVID-19 MESHD, the disease caused by SAR-CoV-2. Here, we show that the 73-amino-acid protein encoded by ORF9c PROTEIN of the viral genome contains a putative transmembrane domain, interacts with membrane proteins in multiple cellular compartments, and impairs antiviral processes in a lung epithelial cell line. Proteomic, interactome, and transcriptomic analyses, combined with bioinformatic analysis, revealed that expression of only this highly unstable small viral protein impaired interferon signaling, antigen presentation, and complement signaling, while inducing IL-6 signaling. Furthermore, we showed that interfering with ORF9c PROTEIN degradation by either proteasome inhibition or inhibition of the ATPase VCP blunted the effects of ORF9c PROTEIN. Our study indicated that ORF9c PROTEIN enables immune evasion and coordinates cellular changes essential for the SARS-CoV-2 life cycle. One-sentence summarySARS-CoV-2 ORF9c PROTEIN is the first human coronavirus protein localized to membrane, suppressing antiviral response, resembling full viral infection.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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